CA2495378A1 - Method for characterizing biomolecules utilizing a result driven strategy - Google Patents
Method for characterizing biomolecules utilizing a result driven strategy Download PDFInfo
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- CA2495378A1 CA2495378A1 CA002495378A CA2495378A CA2495378A1 CA 2495378 A1 CA2495378 A1 CA 2495378A1 CA 002495378 A CA002495378 A CA 002495378A CA 2495378 A CA2495378 A CA 2495378A CA 2495378 A1 CA2495378 A1 CA 2495378A1
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- mass
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- H—ELECTRICITY
- H01—ELECTRIC ELEMENTS
- H01J—ELECTRIC DISCHARGE TUBES OR DISCHARGE LAMPS
- H01J49/00—Particle spectrometers or separator tubes
- H01J49/004—Combinations of spectrometers, tandem spectrometers, e.g. MS/MS, MSn
-
- G—PHYSICS
- G01—MEASURING; TESTING
- G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
- G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
- G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
- G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
- G01N33/68—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids
- G01N33/6803—General methods of protein analysis not limited to specific proteins or families of proteins
-
- H—ELECTRICITY
- H01—ELECTRIC ELEMENTS
- H01J—ELECTRIC DISCHARGE TUBES OR DISCHARGE LAMPS
- H01J49/00—Particle spectrometers or separator tubes
- H01J49/0027—Methods for using particle spectrometers
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- G—PHYSICS
- G01—MEASURING; TESTING
- G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
- G01N30/00—Investigating or analysing materials by separation into components using adsorption, absorption or similar phenomena or using ion-exchange, e.g. chromatography or field flow fractionation
- G01N30/02—Column chromatography
- G01N30/84—Preparation of the fraction to be distributed
- G01N2030/8411—Intermediate storage of effluent, including condensation on surface
- G01N2030/8417—Intermediate storage of effluent, including condensation on surface the store moving as a whole, e.g. moving wire
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- Bioinformatics & Computational Biology (AREA)
- Microbiology (AREA)
- Bioinformatics & Cheminformatics (AREA)
- Proteomics, Peptides & Aminoacids (AREA)
- Medicinal Chemistry (AREA)
- Biochemistry (AREA)
- General Health & Medical Sciences (AREA)
- General Physics & Mathematics (AREA)
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- Other Investigation Or Analysis Of Materials By Electrical Means (AREA)
- Preparation Of Compounds By Using Micro-Organisms (AREA)
- Investigating Or Analysing Biological Materials (AREA)
Abstract
In various embodiments, the methods for analyzing a sample are provided utilizing a result dependent acquisition strategy. In various embodiments, methods for analyzing a sample are provided wherein the sample is first analyzed by MALDI and MS to produce a first result that is then used to determine a second analysis that is used to analyze the sample again by MALDI
and MS/MS or MSn to produce a second result.
and MS/MS or MSn to produce a second result.
Claims (30)
1. A method for analyzing a sample containing biomolecules comprising the steps of providing a plurality of sample portions of a sample containing biomolecules;
acquiring one or more mass spectra of at least one of the sample portions;
analyzing the one or more mass spectra using at least one of an expression dependent based analysis, a mass spectrometric data based analysis, and a search results based analysis;
selecting one or more mass-to-charge ratio ranges based on the analysis of the one or more mass spectra;
acquiring a fragmentation spectrum of at least one of the sample portions at one or more of the selected one or more mass-to-charge ratio ranges;
comparing the fragmentation spectrum of at least one of the selected one or more mass-to-charge ratio ranges to a database of known or predicted fragmentation mass spectra; and determining whether a biomolecule is present in the sample based on the comparison.
acquiring one or more mass spectra of at least one of the sample portions;
analyzing the one or more mass spectra using at least one of an expression dependent based analysis, a mass spectrometric data based analysis, and a search results based analysis;
selecting one or more mass-to-charge ratio ranges based on the analysis of the one or more mass spectra;
acquiring a fragmentation spectrum of at least one of the sample portions at one or more of the selected one or more mass-to-charge ratio ranges;
comparing the fragmentation spectrum of at least one of the selected one or more mass-to-charge ratio ranges to a database of known or predicted fragmentation mass spectra; and determining whether a biomolecule is present in the sample based on the comparison.
2. The method of claim 1, wherein the biomolecules comprise at least one of proteins and peptides.
3. The method of claim 1, wherein the step of acquiring one or more mass spectra comprises:
ionizing at least a portion of the biomolecules in a sample portion using matrix assisted laser desorption ionization; and acquiring one or more mass spectra using a mass spectrometer.
ionizing at least a portion of the biomolecules in a sample portion using matrix assisted laser desorption ionization; and acquiring one or more mass spectra using a mass spectrometer.
4. The method of claim 3, wherein the mass spectrometer comprises a time-of-flight mass spectrometer.
5. The method of claim 1, wherein the step of analyzing the one or more mass spectra comprises determining an expression level ratio between one or more differentially labeled biomolecules in the sample portion.
6. The method of claim 5, wherein the step of selecting one or more mass-to-charge ratio ranges comprises selecting one or more mass-to-charge ratio ranges based on the expression level ratios of a mass signal in the one or more mass spectra.
7. The method of claim 5, further comprising a step of compensating for sample bias in one or more expression level ratios.
8. The method of claim 1, wherein the step of analyzing the one or more mass spectra comprises determining a signal intensity and a signal-to-noise ratio for the one or more mass signals in one or more mass spectra.
9. The method of claim 8, wherein the step of selecting one or more mass-to-charge ratio ranges comprises selecting one or more mass-to-charge ratio ranges based on the signal intensity and a signal-to-noise ratio for one or more mass signals in the one or more mass spectra.
10. The method of claim 1, wherein the step of analyzing the one or more mass spectra comprises comparing of at least a portion of one or more of the one or more mass spectra to one or more known or predicted mass spectra to assign one or more biomolecules as potential identifications of one or mass signals in the one or more mass spectra.
11. The method of claim 10, wherein the step of selecting one or more mass-to-charge ratio ranges comprises selecting one or more mass-to-charge ratio ranges based on a confidence level associated with the one or more biomolecules assigned as potential identifications of one or mass signals in the one or more mass spectra.
12. The method of claim 10, wherein the step of analyzing the one or more mass spectra comprises comparing of at least a portion of one or more of the one or more mass spectra to one or more known or predicted mass spectra to assign one or more biomolecules as potential identifications of one or mass signals in the one or more mass spectra using a peptide mass fingerprinting technique.
13. The method of claim 1, wherein the step of acquiring a fragmentation spectrum comprises:
ionizing at least a portion of the biomolecules in a sample portion using matrix assisted laser desorption ionization to produce sample ions;
separating sample ions using a first mass spectrometer;
fragmenting at least a portion of the sample ions in the selected one or more mass-to-charge ratio ranges; and acquiring a fragmentation spectrum using a second mass spectrometer.
ionizing at least a portion of the biomolecules in a sample portion using matrix assisted laser desorption ionization to produce sample ions;
separating sample ions using a first mass spectrometer;
fragmenting at least a portion of the sample ions in the selected one or more mass-to-charge ratio ranges; and acquiring a fragmentation spectrum using a second mass spectrometer.
14. The method of claim 13, wherein the first mass spectrometer and second mass spectrometer comprises a tandem time-of-flight mass spectrometer system.
15. An article of manufacture comprising a computer-readable media with computer- readable instructions embodied thereon for performing the method of claim 1.
16. A method for analyzing a sample containing proteins comprising the steps of providing a plurality of sample portions each comprising a first sample containing at least one of peptides and proteins and a second sample containing at least one of peptides and proteins, at least a portion of the biomolecules in the first sample and the second sample being differentially labeled with an isotope coded reagent;
acquiring one or more mass spectra of at least one of the sample portions;
determining an expression level ratio between one or more differentially labeled biomolecules in the sample portion;
selecting one or more mass-to-charge ratio ranges based on the expression level ratios of a mass signal in the one or more mass spectra;
acquiring a fragmentation spectrum of at least one of the sample portions at one or more of the selected one or more mass-to-charge ratio ranges;
comparing the fragmentation spectrum of at least one of the selected one or more mass-to-charge ratio ranges to a database of known or predicted fragmentation mass spectra; and determining whether a biomolecule is present in the sample based on the comparison.
acquiring one or more mass spectra of at least one of the sample portions;
determining an expression level ratio between one or more differentially labeled biomolecules in the sample portion;
selecting one or more mass-to-charge ratio ranges based on the expression level ratios of a mass signal in the one or more mass spectra;
acquiring a fragmentation spectrum of at least one of the sample portions at one or more of the selected one or more mass-to-charge ratio ranges;
comparing the fragmentation spectrum of at least one of the selected one or more mass-to-charge ratio ranges to a database of known or predicted fragmentation mass spectra; and determining whether a biomolecule is present in the sample based on the comparison.
17. The method of claim 16, wherein the step of acquiring one or more mass spectra comprises:
ionizing at least a portion of the biomolecules in a sample portion using matrix assisted laser desorption ionization; and acquiring one or more mass spectra using a mass spectrometer.
ionizing at least a portion of the biomolecules in a sample portion using matrix assisted laser desorption ionization; and acquiring one or more mass spectra using a mass spectrometer.
18. The method of claim 17, wherein the mass spectrometer comprises a time-of flight mass spectrometer.
19. The method of claim 16, further comprising a step of compensating for sample bias in one or more expression level ratios.
20. The method of claim 16, further comprising the step of determining a signal intensity and a signal-to-noise ratio for one or more mass signals in the one or more mass spectra
21. The method of claim 20, wherein the step of selecting one or more mass-to-charge ratio ranges further comprises selecting one or more mass-to-charge ratio ranges based on the signal intensity and a signal-to-noise ratio for one or more mass signals in the mass spectrum.
22. The method of claim 16, further comprising the step of comparing of at least a portion of one or more of the one or more mass spectra to one or more known or predicted mass spectra to assign one or more biomolecules as potential identifications of one or mass signals in the one or more mass spectra.
23. The method of claim 22, wherein the step of selecting one or more mass-to-charge ratio ranges further comprises selecting one or more mass-to-charge ratio ranges based on a confidence level associated with the one or more biomolecules assigned as potential identifications of one or mass signals in the one or more mass spectra.
24. The method of claim 22, wherein the step of analyzing the one or more mass spectra comprises comparing of at least a portion of one or more of the one or more mass spectra to one or more known or predicted mass spectra to assign one or more biomolecules as potential identifications of one or mass signals in the one or more mass spectra using a peptide mass fingerprinting technique.
25. The method of claim 16, wherein the step of acquiring a fragmentation spectrum comprises:
ionizing at least a portion of the biomolecules in a sample portion using matrix assisted laser desorption ionization to produce sample ions;
separating sample ions using a first mass spectrometer;
fragmenting at least a portion of the sample ions in the selected one or more mass-to-charge ratio ranges; and acquiring a fragmentation spectrum using a second mass spectrometer.
ionizing at least a portion of the biomolecules in a sample portion using matrix assisted laser desorption ionization to produce sample ions;
separating sample ions using a first mass spectrometer;
fragmenting at least a portion of the sample ions in the selected one or more mass-to-charge ratio ranges; and acquiring a fragmentation spectrum using a second mass spectrometer.
26. The method of claim 25, wherein the first mass spectrometer and second mass spectrometer comprises a tandem time-of-flight mass spectrometer system.
27. An article of manufacture comprising a computer-readable media with computer-readable instructions embodied thereon for performing the method of claim 16.
28. A method for analyzing a sample for at least one biomolecule comprising the steps of depositing at least one sample portion on a solid support;
vaporizing at least a portion of the sample portion by matrix assisted laser desorption ionization to form a first vaporized ionized sample;
processing at least a portion of the first vaporized ionized sample with a mass spectrometry apparatus to determine a first data set comprising a list of ion abundances as a function of ion mass-to-charge ratio of the first vaporized ionized sample;
comparing the first data set with at least one of a second data set which identifies biomolecules by ion abundance as a function of ion mass-to-charge ratio;
selecting one or more ion mass-to-charge ratio ranges for further analysis based on the comparison;
vaporizing at least another portion of the biological sample by matrix assisted laser desorption ionization to form a second vaporized ionized sample;
processing at least a portion of the second vaporized ionized sample with a mass spectrometry apparatus adjusted based on the first data set thereby to determine a third data set comprising a list of ion abundance as a function of ion mass-to-charge ratio of the second vaporized ionized sample; and performing at least one of the steps of:
comparing the third data set with a fourth data set which identifies biomolecules by ion abundance as a function of ion mass-to-charge ratio, and using the identified biomolecules data and the first data set to obtain quantitative information on the one or more biomolecules in the sample.
vaporizing at least a portion of the sample portion by matrix assisted laser desorption ionization to form a first vaporized ionized sample;
processing at least a portion of the first vaporized ionized sample with a mass spectrometry apparatus to determine a first data set comprising a list of ion abundances as a function of ion mass-to-charge ratio of the first vaporized ionized sample;
comparing the first data set with at least one of a second data set which identifies biomolecules by ion abundance as a function of ion mass-to-charge ratio;
selecting one or more ion mass-to-charge ratio ranges for further analysis based on the comparison;
vaporizing at least another portion of the biological sample by matrix assisted laser desorption ionization to form a second vaporized ionized sample;
processing at least a portion of the second vaporized ionized sample with a mass spectrometry apparatus adjusted based on the first data set thereby to determine a third data set comprising a list of ion abundance as a function of ion mass-to-charge ratio of the second vaporized ionized sample; and performing at least one of the steps of:
comparing the third data set with a fourth data set which identifies biomolecules by ion abundance as a function of ion mass-to-charge ratio, and using the identified biomolecules data and the first data set to obtain quantitative information on the one or more biomolecules in the sample.
29. The method, of any one of claims 28, wherein at least one first vaporized biomolecule having a low concentration in the sample is processed as a second vaporized ionized sample prior to processing a biomolecule having a higher concentration in the sample than the first vaporized biomolecule.
30. An article of manufacture comprising a computer-readable media with computer-readable instructions embodied thereon for performing the method of claim 28.
Applications Claiming Priority (3)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| US40557802P | 2002-08-22 | 2002-08-22 | |
| US60/405,578 | 2002-08-22 | ||
| PCT/US2003/026471 WO2004019035A2 (en) | 2002-08-22 | 2003-08-22 | Method for characterizing biomolecules utilizing a result driven strategy |
Publications (2)
| Publication Number | Publication Date |
|---|---|
| CA2495378A1 true CA2495378A1 (en) | 2004-03-04 |
| CA2495378C CA2495378C (en) | 2011-03-01 |
Family
ID=31946899
Family Applications (1)
| Application Number | Title | Priority Date | Filing Date |
|---|---|---|---|
| CA2495378A Expired - Fee Related CA2495378C (en) | 2002-08-22 | 2003-08-22 | Method for characterizing biomolecules utilizing a result driven strategy |
Country Status (8)
| Country | Link |
|---|---|
| US (1) | US6940065B2 (en) |
| EP (1) | EP1530721B1 (en) |
| JP (1) | JP4160558B2 (en) |
| AT (1) | ATE418729T1 (en) |
| AU (1) | AU2003262824B2 (en) |
| CA (1) | CA2495378C (en) |
| DE (1) | DE60325482D1 (en) |
| WO (1) | WO2004019035A2 (en) |
Cited By (1)
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|---|---|---|---|---|
| WO2006128297A1 (en) * | 2005-06-03 | 2006-12-07 | Mds Inc. Doing Business Through Its Mds Sciex Division | System and method for analysis of compounds using a mass spectrometer |
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| US11393666B2 (en) | 2019-12-19 | 2022-07-19 | Thermo Finnigan Llc | Automatic MS-N characterization of mass spectrometric “dark matter” |
| EP4172616A1 (en) | 2020-06-29 | 2023-05-03 | Waters Technologies Corporation | Chromatographic dimension selection in multidimensional liquid chromatography |
| JP7514789B2 (en) | 2021-04-08 | 2024-07-11 | 日本電子株式会社 | Method for detecting virus-derived proteins, mass spectrum processing device, and mass analysis system |
| GB202405611D0 (en) | 2023-05-03 | 2024-06-05 | Bruker Daltonics Gmbh & Co Kg | Method of bioanalytical analysis utilizing ion spectrometry, including mass analysis |
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| US5625184A (en) | 1995-05-19 | 1997-04-29 | Perseptive Biosystems, Inc. | Time-of-flight mass spectrometry analysis of biomolecules |
| GB9624927D0 (en) * | 1996-11-29 | 1997-01-15 | Oxford Glycosciences Uk Ltd | Gels and their use |
| US6596529B1 (en) | 1997-05-02 | 2003-07-22 | Uab Research Foundation | Manipulation of negative stranded RNA viruses by rearrangement of their genes and uses thereof |
| US6175112B1 (en) | 1998-05-22 | 2001-01-16 | Northeastern University | On-line liquid sample deposition interface for matrix assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectroscopy |
| US6348688B1 (en) | 1998-02-06 | 2002-02-19 | Perseptive Biosystems | Tandem time-of-flight mass spectrometer with delayed extraction and method for use |
| US6428956B1 (en) * | 1998-03-02 | 2002-08-06 | Isis Pharmaceuticals, Inc. | Mass spectrometric methods for biomolecular screening |
| CA2255122C (en) | 1998-12-04 | 2007-10-09 | Mds Inc. | Improvements in ms/ms methods for a quadrupole/time of flight tandem mass spectrometer |
| US6799121B2 (en) * | 2000-03-30 | 2004-09-28 | York University | Sequencing of peptides by mass spectrometry |
| AU2001286059A1 (en) * | 2000-09-08 | 2002-03-22 | Oxford Glycosciences (Uk) Ltd. | Automated identification of peptides |
| JP2005504263A (en) * | 2001-02-01 | 2005-02-10 | シファーゲン バイオシステムズ， インコーポレイテッド | Improved method for protein identification, characterization and sequencing by tandem mass spectrometry |
| US6977732B2 (en) | 2002-12-26 | 2005-12-20 | National Taiwan University | Miniature three-dimensional contour scanner |
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- 2003-08-22 AT AT03793347T patent/ATE418729T1/en not_active IP Right Cessation
- 2003-08-22 US US10/646,371 patent/US6940065B2/en not_active Expired - Fee Related
- 2003-08-22 JP JP2004529924A patent/JP4160558B2/en not_active Expired - Fee Related
- 2003-08-22 AU AU2003262824A patent/AU2003262824B2/en not_active Ceased
- 2003-08-22 DE DE60325482T patent/DE60325482D1/en not_active Expired - Lifetime
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- 2003-08-22 EP EP03793347A patent/EP1530721B1/en not_active Expired - Lifetime
Cited By (1)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| WO2006128297A1 (en) * | 2005-06-03 | 2006-12-07 | Mds Inc. Doing Business Through Its Mds Sciex Division | System and method for analysis of compounds using a mass spectrometer |
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| EP1530721A2 (en) | 2005-05-18 |
| ATE418729T1 (en) | 2009-01-15 |
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| EP1530721B1 (en) | 2008-12-24 |
| AU2003262824B2 (en) | 2007-08-23 |
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| JP4160558B2 (en) | 2008-10-01 |
| WO2004019035A2 (en) | 2004-03-04 |
| CA2495378C (en) | 2011-03-01 |
| WO2004019035A3 (en) | 2005-02-17 |
| US20040108452A1 (en) | 2004-06-10 |
| DE60325482D1 (en) | 2009-02-05 |
| US6940065B2 (en) | 2005-09-06 |
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